Our son played baseball in the ACC and majored in mechanical engineering. There are several old posts detailing his experiences, so I won't bore you with all of those stories again. Our DAUGHTER rowed at the same ACC school for 2.5 yrs before giving it up due to shoulder issues. She also double-majored in Philosophy and Biology. (Philosophy being her first love, Biology being a way to keep her options open). She really did not consider med school until her senior year in college.
It is very difficult to compare engineering vs. pre-med paths, even with two kids I know so well. In fact, as I write this, I keep going back and forth with regard to which is more difficult. However, my gut feeling is that engineering is probably a slightly more difficult path. That is primarily because of the time involved with the engineering major. Your experience/opinion may be totally different. As with all things, it really depends on the kid.
Baseball undoubtedly had some effect on son's GPA, but so did his other extra-curriculars. Rowing probably affected daughter's GPA a little as well, but nothing major.
GPA is VERY important for med school. My daughter's was somewhat marginal, in the 3.65 neighborhood. Most of her classmates in med school had much better undergraduate grades. What they didn't have was a 37 on the MCAT.
As someone else pointed out, med schools do like kids with non-traditional majors, provided they have all of the necessary core courses and MCAT scores. I'd say half of daughter's med school classmates had traditional majors like Biology and Chemistry. The rest were all across the board in terms of majors. They also like kids with work histories, something that's hard to get while playing baseball. I know one kid that had good enough grades and MCAT score, but they told him he needed to get some clinical experience and reapply. He did, and was accepted. Of course, if his SAT and/or MCAT had been higher, he probably would have been admitted the first time.
Some schools, like the one my kids attended, do very little to accommodate kids with time consuming majors. However, others do an excellent job. Wofford College is a great example. There are currently 4 former Wofford College baseball players in medical school. If I am not mistaken, they all started Wofford the same year. Wofford bends over backward to help kids like this.
The bottom line is baseball and pre-med are doable. It just depends on the kid.